Merge branch 'master' of git.embl.de:ckerr/galumph

README.md

 # GALUMPH #
 
-Calculate ALM (scattering amplitude decomposed into spherical harmonics) using GPU acceleration.
+Calculate ALM (scattering amplitude decomposed into spherical harmonics) at Hyperspeed using GPU acceleration.
 
 This is a preliminary implementation using PyOpenCL.
+
+Example code:
+```python
+import numpy as np
+import Bio.PDB
+import periodictable
+import galumph
+
+
+NS = 4096   # Number of S values at which to calculate the scattering
+smax = 1.0  # Maximum S value
+LMAX = 63   # Maximum harmonic order to use for the calculations
+
+## Initialise the S array and allocate the ALM storage on the GPU
+s = np.linspace(0, smax, NS)
+atomalm = galumph.AtomAlm(LMAX, s)
+
+## Use Bio.PDB to read the structure and periodictable to calculate the atomic form factors
+pdb = Bio.PDB.PDBParser().get_structure("6lyz", "6lyz.pdb")
+xyz = np.array([aa.get_vector().get_array() for aa in pdb.get_atoms()])
+ff = np.array([periodictable.elements.symbol(aa.element).xray.f0(s) for aa in pdb.get_atoms()])
+
+## Run the GPU calculation
+atomalm.add_many_atoms(xyz, ff)
+Icalc = atomalm.sum_intensity()
+```
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